Nesting master pages is common practice, for direction on how to accomplish nesting see http://msdn.microsoft.com/en-us/library/wtxbf3hh.aspx or http://www.asp.net/learn/3.5-videos/video-256.aspx.
One of the cooler scenarios that ASP.NET
2.0 supports is the ability to have "nested master pages" - where you
can create a root master page for a site that defines a site's overall
layout, and then create nested master pages that are based on the root
master and further customize the layout (for example: you could create
a SingleColumn.Master and TwoColumn.Master that defined 1 or 2 column
layout structures based on the root master template). This nested
master page feature is extremely flexible, and enables developers and
designers to quickly and very cleanly make changes to the layout and
organization of a site with minimal code changes and no content
duplication. - http://weblogs.asp.net/scottgu/archive/2007/07/09/vs-2008-nested-master-page-support.aspx.
The parent master page contains the header/menu/footer for my site with a content area in the middle of the page. I've purchased the DashCommerce Commercial License, I've stripped the header/footer from DashCommerce's site.master and nested it in my parent master page placing the store inside the look/layout of my site maintaining my site's navigation.
I'm happy to send you the stripped down example parent master page (site1.master) and the modified nested dashcommerce master page (site.master) and PageBuilder.cs if you provide an email address or email me at the email address attached to my DashCommerce.org account.
Thank you,
Jason